The Frenchman was left badly battered and bruised in a testing crash only days before the season opener.
On Monday, de Puniet fell in the final pre-season test but was left with nothing broken but badly bruised and with extensive muscle damage.
However, despite the injuries, he finished seventh fastest in the second race as well as being on track for a race one top ten until an altercation with MV Agusta rider Leon Camier.
"It was a horrible Sunday for me, I was in a lot of pain and the first race was a disaster. After six laps I was not able to ride because I had pain everywhere, plus arm pump, so it was impossible to brake or to accelerate, and I tried to manage a good position – I think I was ninth and should have been able to finish tenth. Unfortunately Camier hit me, I went straight on and finished 17th so I'm a little bit disappointed," said de Puniet.
"I was worried again about my physical condition for race two but luckily I was able to manage it better, and I finished seventh. Until the middle of the race I was only four seconds from the lead but after that I started to struggle again, I tried to keep a good rhythm and finished seventh, which is a good result in this condition.
"Without the no score in the first race it would have been possible to be seventh in the Championship, I'm 11th which is a shame but after everything this week this is not so bad. Now it's time for me to recover and get fit for Thailand," he added.